8BQH

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 min


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829324% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
238.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.361α = 90
b = 127.456β = 90
c = 128.952γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6190.6594.140.9969.55.794816
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.780.6555

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6SDR1.6190.6594816477868.5170.1520.15090.175419.364
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.132-0.062-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.373
r_dihedral_angle_4_deg19.159
r_dihedral_angle_3_deg13.409
r_lrange_it7.282
r_lrange_other7.264
r_dihedral_angle_1_deg6.894
r_scangle_it6.18
r_scangle_other6.18
r_scbond_other4.572
r_scbond_it4.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.373
r_dihedral_angle_4_deg19.159
r_dihedral_angle_3_deg13.409
r_lrange_it7.282
r_lrange_other7.264
r_dihedral_angle_1_deg6.894
r_scangle_it6.18
r_scangle_other6.18
r_scbond_other4.572
r_scbond_it4.56
r_mcangle_it3.913
r_mcangle_other3.913
r_mcbond_other2.927
r_mcbond_it2.926
r_angle_refined_deg1.601
r_angle_other_deg1.452
r_symmetry_xyhbond_nbd_refined0.286
r_nbd_other0.213
r_nbd_refined0.211
r_symmetry_nbd_other0.197
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.146
r_symmetry_nbd_refined0.142
r_chiral_restr0.089
r_symmetry_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9126
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms230

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction